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Human vs Squirrel LastZ alignments

Human (Homo sapiens, GRCh37) and Squirrel (Spermophilus tridecemlineatus, spetri2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 67. Human was used as the reference species. After running LastZ, the raw LastZ alignment blocks are chained according to their location in both genomes. During the final netting process, the best sub-chain is chosen in each region on the reference species.

Full list of pairwise alignments

Configuration parameters

Gap open penalty (O) 400
Gap extend penalty (E) 30
HSP threshold (K) 3000
Threshold for gapped extension (L) 3000
Threshold for alignments between gapped alignment blocks (H) 2200
Masking count (M)
Seed and Transition value (T) 1
Additional parameters --ambiguous=iupac
Scoring matrix (Q) Default

Chunking parameters

Human Squirrel
Chunk size 0 10,100,000
Overlap 0 100,000
Group set size 0 10,100,000
Masking options {default_soft_masking => 1}

Results

Number of alignment blocks: 1977251

Genome coverage(bp) Coding exon coverage (bp)
Human
1,479,659,180 out of 3,098,825,702 33,856,460 out of 35,155,918
Squirrel
1,379,279,831 out of 2,478,393,770 27,433,177 out of 28,885,868